[BioRuby] Bio::GFF::GFF3 error

[graham etherington (TSL)]

Thanks Marjan,
That did the trick.
Regards,
Graham

Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601





On 06/11/2013 12:42, "Marjan Povolni" <marian.povolny at gmail.com> wrote:

>Hello,
>
>
>I managed to recreate the issue on Ubuntu with ruby-2.0.0-p247, with bio
>version 1.4.3 gem, and what solved the issue was updating the bio gem:
>
>
>gem update bio
>
>
>That should update the gem to version 1.4.3.0001 (latest), and on my
>setup the error message doesn't appear anymore.
>
>
>
>Best regards,
>Marjan
>
>
>
>
>On Wed, Nov 6, 2013 at 11:47 AM, graham etherington (TSL)
><graham.etherington at sainsbury-laboratory.ac.uk> wrote:
>
>Hi,
>I¹m getting some strange behaviour when trying to create a Bio::GFF::GFF3
>object from a gff file.
>
>Here is my test code that throws the error (test_gff.rb):
>
>require 'bio'
>Bio::GFF::GFF3.new(File.read("gene.gff"))
>
>
>Here is my gff file (gene.gff) (validated at
>http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online):
>
>##gff-version 3
>##sequence-region ctg123 1 1497228
>ctg123  .       gene    900     9900    .       +       .
>ID=gene00001;Name=EDEN
>ctg123  .       gene    10900   19900   .       -       .
>ID=gene00002;Name=EDEN2
>
>
>
>
>Here is the error:
>test_gff.rb:2:in `<main>':
>/Users/ethering/.rvm/gems/ruby-2.0.0-p247/gems/bio-1.4.3/lib/bio/db/gff.rb
>:
>238: invalid multibyte escape: /[\t\r\n\x00-\x1f\x7f\xfe\xff]/
>(SyntaxError)
>invalid multibyte escape: /[\s\"\;\t\r\n\x00-\x1f\x7f\xfe\xff]/
>
>
>
>There are two things I¹m confused at here.
>1. I¹m getting errors for a validated gff file.
>2. The errors thrown are coming from the GFF2 code in bio/db/gff.db, as
>follows (line numbers provided):
>
>237 # prohibited characters in GFF2 columns
>    238         PROHIBITED_GFF2_COLUMNS = /[\t\r\n\x00-\x1f\x7f\xfe\xff]/
>    239
>    240         # prohibited characters in GFF2 attribute tags
>    241         PROHIBITED_GFF2_TAGS =
>/[\s\"\;\t\r\n\x00-\x1f\x7f\xfe\xff]
>
>
>ruby -v
>ruby 2.0.0p247 (2013-06-27 revision 41674) [x86_64-darwin12.5.0]
>
>
>Any suggestions?
>Many thanks,
>Graham
>
>
>
>Dr. Graham Etherington
>Bioinformatics Support Officer,
>The Sainsbury Laboratory,
>Norwich Research Park,
>Norwich NR4 7UH.
>UK
>Tel: +44 (0)1603 450601
>
>
>
>
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>BioRuby at lists.open-bio.org
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>
>
>
>
>